発表論文

2021

原著論文
  1. Kunihiko Kaneko and Chikara Furusawa "Direction and Constraint in Phenotypic Evolution: Dimension Reduction and Global Proportionality in Phenotype Fluctuation and Responses". arXiv:2102.03025

2020

原著論文
  1. Tomoya Maeda*, Junichiro Iwasawa*, Hazuki Kotani, Natsue Sakata, Masako Kawada, Takaaki Horinouchi, Aki Sakai, Kumi Tanabe, and Chikara Furusawa "High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli". Nature Communications 11, 5970 (2020).
  2. Daisuke Imoto, Nen Saito, Akihiko Nakajima, Gen Honda, Motohiko Ishida, Toyoko Sugita, Sayaka Ishihara, Koko Katagiri, Chika Okimura, Yoshiaki Iwadate, Satoshi Sawai "Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space". bioRxiv doi: 10.1101/2020.09.06.285411
  3. Gen Honda, Nen Saito, Taihei Fujimori, Hidenori Hashimura, Mitsuru J. Nakamura, Akihiko Nakajima, Satoshi Sawai "Micro-topographical guidance of macropinocytic signaling patches". bioRxiv doi: 10.1101/2020.08.29.273185
  4. Nen Saito, Satoshi Sawai "Three-dimensional morphodynamics simulations of macropinocytic cups". bioRxiv doi: 10.1101/2020.06.22.165027
  5. Chikara Furusawa, Naoki Irie "Toward understanding of evolutionary constraints: experimental and theoretical approaches". Biophys Rev (2020).
  6. Takaaki Horinouchi, Chikara Furusawa "Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis". Biophys Rev (2020).
  7. Ryudo Ohbayashi, Shunsuke Hirooka, Ryo Onuma, Yu Kanesaki, Yuu Hirose, Yusuke Kobayashi, Takayuki Fujiwara, Chikara Furusawa, Shin-ya Miyagishima "Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria". Frontiers in Microbiology 11, 786 (2020).
  8. Takaaki Horinouchi, Tomoya Maeda, Hazuki Kotani, and Chikara Furusawa "Suppression of antibiotic resistance evolution by single-gene deletion". Scientific Reports 10, 4178 (2020).
  9. Jumpei F. Yamagishi, Nen Saito, Kunihiko Kaneko, "Advantage of Leakage of Essential Metabolites for Cells" Physical Review Letters, 124, 4, 048101 (2020),

2019

原著論文
  1. Atsushi Shibai, Katsuya Satoh, Masako Kawada, Hazuki Kotani, Issay Narumi, Chikara Furusawa, "Complete Genome Sequence of a Radioresistant Bacterial Strain, Deinococcus grandis ATCC 43672" Microbiology resource announcements, 8, 45 (2019)
  2. Atsushi Shibai, Tomoya Maeda, Masako Kawada, Hazuki Kotani, Natsue Sakata, Chikara Furusawa, "Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155" Microbiology resource announcements, 8, 32 (2019)
  3. Tomoya Maeda, Takaaki Horinouchi, Natsue Sakata, Aki Sakai, Chikara Furusawa, "High-throughput identification of the sensitivities of an Escherichia coli recA mutant strain to various chemical compounds" The Journal of antibiotics 72, 7, 566 (2019)
  4. Tomoyuki Yamaguchi, Shunsuke Teraguchi, Chikara Furusawa, Hiroaki Machiyama, Tomonobu M Watanabe, Hideaki Fujita, Shimon Sakaguchi, Toshio Yanagida, "Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance" International immunology, dxz043 (2019)

2018

原著論文
  1. Chikara Furusawa, Takaaki Horinouchi, Tomoya Maeda, "Toward prediction and control of antibiotic-resistance evolution" Current opinion in biotechnology 54, 45-49 (2018)
  2. Takaaki Horinouchi, Tomoya Maeda, Chikara Furusawa, "Understanding and engineering alcohol-tolerant bacteria using OMICS technology" World Journal of Microbiology and Biotechnology 34, 11, 157 (2018)
  3. Takahiro Komori, Atsushi Shibai, Hiromi Saito, Yuya Akeno, Arno Germond, Takaaki Horinouchi, Chikara Furusawa, Saburo Tsuru, "Enhancement of K-strategy evolution in histidine utilization using a container with compartments" Genes to Cells 23, 10, 893-903 (2018)
  4. Kazuko Okamoto, Arno Germond, Hideaki Fujita, Chikara Furusawa, Yasushi Okada, Tomonobu M Watanabe, "Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation" Scientific reports 8, 1, 11965 (2018)
  5. Arno Germond, Taro Ichimura, Takaaki Horinouchi, Hideaki Fujita, Chikara Furusawa, Tomonobu M Watanabe, "Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli" Communications biology 1, 1, 85 (2018)
  6. Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu, "Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain" Biotechnology and bioengineering 115, 6, 1542-1551 (2018)
  7. Kunihiko Kaneko, Chikara Furusawa, "Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics" Annual review of biophysics 47, 273-290 (2018)
  8. Takashi Hirasawa, Masaki Saito, Katsunori Yoshikawa, Chikara Furusawa, Hiroshi Shmizu, "Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin Induced Glutamic Acid Production" Biotechnology journal 13, 5, 1700612 (2018)
  9. Chikara Furusawa, Kunihiko Kaneko, "Formation of dominant mode by evolution in biological systems" Physical Review E 97, 4 (2018)

2017

原著論文
  1. S. Suzuki, T. Horinouchi, C. Furusawa, "Phenotypic changes associated with the fitness cost in antibiotic resistant Escherichia coli strains." Meth. Mol. Biol., 1520, 263
  2. N. Saito, K. Kaneko, "Embedding dual function into molecular motors through collective motion." Sci. Rep., 7

2016

原著論文
  1. S. Suzuki, T. Horinouchi, C. Furusawa, "Expression profiling of antibiotic resistant bacteria obtained by laboratory evolution."Mol. Biosys., 12(2), 414
  2. C. Furusawa and T. Yamaguchi, "Robust and Accurate Discrimination of Self/Non-Self Antigen Presentations by Regulatory T Cell Suppression."PLoS One, 11(9), e0163134
  3. N. Saito, Y. Sughiyama and K. Kaneko, "Motif Analysis for Small-Number Effects in Chemical Reaction Dynamics."Jour. Chem. Phys., 145, 094111
  4. J. F. Yamagishi, N. Saito and K. Kaneko, "Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates." PLoS Comput. Biol., 12(10), e1005042.
総説・解説
  1. 古澤力, 鈴木真吾, 堀之内貴明"大腸菌進化実験を用いた遺伝子発現量からの抗生物質耐性メカニズムの解 ",バイオサイエンスとインダストリー, 72(2), 138-140

2015

原著論文
  1. K. Kaneko, C. Furusawa, T. Yomo, "Universal Relationship in Gene-Expression Changes for Cells in Steady-Growth State." Phys. Rev. X, 5, 011014
  2. T. Horinouchi, S. Suzuki, T. Hirasawa, N. Ono, T. Yomo, H. Shimizu, C. Furusawa, "Phenotypic convergence in bacterial adaptive evolution to ethanol stress." BMC Evol. Biol., 15, 180
  3. K. Yoshikawa, S. Aikawa, Y. Kojima, Y. Toya, C. Furusawa, A. Kondo, H. Shimizu, "Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction." PLoS One, 10(12), e0144430
  4. B.W. Ying, Y. Matsumoto, K. Kitahara, S. Suzuki, N. Ono, C. Furusawa, T. Kishimoto, T. Yomo,"Bacterial transcriptome reorganization in thermal adaptive evolution." BMC Genomics, 16(1), 802
  5. C. Furusawa, K. Kaneko, "Global relationships in fluctuation and response in adaptive evolution."Jour. Roy. Soc. Interface, 12(109), 20150482
  6. S. Suzuki, T. Horinouchi, C. Furusawa, "Suppression of antibiotic resistance acquisition by combined use of antibiotics"Jour. Biosci. Bioeng., 120(4), 467-9
  7. S. Kajihata, F. Matsuda, M. Yoshimi, K. Hayakawa, C. Furusawa, A. Kanda, H. Shimizu, "13C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect." Jour. Biosci.    Bioeng., 120(2), 140-4
  8. T. Miyamoto, C. Furusawa, K. Kaneko, "Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation." PLoS Comp. Biol., 11(8), e1004476
総説・解説
  1. 古澤力,"進化学に残された謎", 進化の謎をゲノムで解く(監修:長谷部光泰), 学研メディカル秀潤社
  2. 堀之内貴明, 古澤力,"適応進化はどのように起こるのか-進化実験によるアプローチ-", 進化の謎をゲノムで解く(監修:長谷部光泰), 学研メディカル秀潤社

2014

原著論文
  1. Shingo Suzuki, Takaaki Horinouchi, and Chikara Furusawa, "Prediction of antibiotic resistance by gene expression profiles." Nature Communications, 5, 5792
  2. Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu,and Chikara Furusawa,"Development of an automated culture system for laboratory evolution"Journal of Laboratory Automation, 19(5), 478-82
  3. Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa and Hiroshi Shimizu, "Increased 3-hydroxypropionic acid production from glycerol, by  modification of central metabolism in Escherichia coli" Microbial Cell Factories, 13, 64
  4. Satoshi Oono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering"Bioinformatics, 30(7), 981-7
  5. T. Nakajima, S. Kajihata, K. Yoshikawa, F. Matsuda, C. Furusawa, T.Hirasawa, H. Shimizu,"Integrated Metabolic Flux and Omics Analysis of Synechocystis sp. PCC 6803 under Mixotrophic and  Photoheterotrophic Conditions" Plant Cell Physiol, 55(9), 1605-12
  6. S. Kajihata, C. Furusawa, F. Matsuda, H. Shimizu, "OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis" Biomed Res Int, 2014, 627014
  7. N. Okahashi, S. Kajihata, C. Furusawa, H. Shimizu, "Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids" Metabolites,4,(2),408-420
  8. Yuto Yamauchi, Takashi Hirasawa, Masato Nishii, Chikara Furusawa, Hiroshi Shimizu, "Enhanced  acetic acid and succinic acid production under microaerobic conditions by?Corynebacterium glutamicum?harboring Escherichia coli transhydrogenase gene pntAB" The Journal of General and Applied Microbiology, 60,(3),112-118
  9. T. Hirasawa, Y. Ida, C. Furusawa, H. Shimizu, "Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction. " Bioengineered, 5,(2),123-128
総説・解説
  1. 堀之内貴明, 古澤力,"適応進化はどのように起こるのか-進化実験によるアプローチ- "細胞工学 Vol.33(6), 666-669 (2014)

2013

原著論文
  1. Takashi Hirasawa, Katsunori Yoshikawa, Aki Ookubo, Chikara Furusawa, Hiroshi Shimizu, "Genome-wide identification of the targets for genetic manipulation to improve l-lactate production by Saccharomyces cerevisiae by using a single-gene deletion strain collection," J. Biotech., 168(2), 185-93 (2013)
  2. Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu, "ArtPathDesign: Rational heterologous pathway design system for the production of nonnative metabolites," Journal of Bioscience and Bioengineering, 116(4), 524-527 (2013)
  3. Chikara Furusawa, Kunihiko Kaneko, "Epigenetic feedback regulation accelerates adaptation and evolution," PLoS One, 8(5), e61251 (2013)
  4. Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu, "Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution," Adv.Biochem. Eng. Biotechnol., 131, 1-23 (2013)
  5. Yoshihiro Ida, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu, "Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction," Applied Microbiology and Biotechnology, 97(11), 4811-4819 (2013)
  6. Katsunori Yoshikawa, Takashi Hirasawa, Kenichi Ogawa, Yuki Hidaka, Tsubasa Nakajima, Chikara Furusawa, Hiroshi Shimizu, "Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions," Biotechnology Journal,8(5), 571-580 (2013)